Sara Patti

Hi all, Any updates on using this to convert a spatial experiment to an anndata object? The data is IMC data. I tried to use ``` writeH5AD(spe, file = out_path)...

Thanks for the quick response! :) Let me check with my supervisor on sharing the data and Ill get back to you

Makes sense! here is a good resource that has the spe object: https://github.com/BodenmillerGroup/ImagingWorkshop2023/tree/main/data https://github.com/BodenmillerGroup/IMCDataAnalysis/tree/main https://bodenmillergroup.github.io/IMCDataAnalysis/index.html This gives the pipeline as well so will provide details on what is in the...

Hi @lazappi, I was trying a dataset in the group, but also tried the dataset that I had shared in #61. I've checked both the dataset from our group as...

Hi @lazappi Please let me know if you can't access it https://drive.google.com/drive/folders/1CuXBWQUPI9hvPxOcl2gmBgHwWRiWo01y?usp=drive_link

Apologies, I thought it was public. Should be public now - please let me know if there is any issues.

Thanks so much! That worked for us! Thank you for making the note about the change in edge weights being set to 1.

Hi, We tired again with another dataset we recently generated and hit a similar/possibly the same issue. We also re-ran it with the original test dataset and got a different...

Hi @lazappi Thanks for getting back to us! Here is the sessionInfo: ``` > sessionInfo() R version 4.3.0 (2023-04-21) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS 14.4.1 Matrix products: default BLAS:...

Solved the problem. You can only have 1 item in colPairs and we had 4 items in there as we ran different several interaction graph algorithms.